mrfseg.pl

MRF-based tissue segmentation pipeline

mrfseg.pl <input_t1.mnc> <output.mask> [options]

DESCRIPTION

mrfseg.pl is a Perl wrapper that runs an MRF (Markov Random Field) based tissue segmentation pipeline on a T1-weighted MRI volume. The pipeline first estimates tissue intensity distributions using gamixture (Gaussian mixture modelling), then applies mrfseg to perform spatially regularized classification. The result is a discrete tissue label mask.

An atlas specification can be supplied to provide tissue priors. A brain mask can be provided to restrict the segmentation to the brain region. A low-resolution mode is available for faster processing at reduced spatial resolution.

OPTIONS

--verbose

Print progress information during processing.

--clobber

Overwrite existing output files.

--mask <mask.mnc>

Specify a brain mask to restrict the segmentation region. The default value is “default”, which uses the mask provided by the atlas.

--atlas <spec>

Specify an atlas directory or specification file for tissue priors.

--lowres

Run the segmentation at low resolution for faster processing.

EXAMPLES

Segment a T1 volume using default settings:

mrfseg.pl input_t1.mnc output_labels.mnc

Segment with a custom brain mask and verbose output:

mrfseg.pl input_t1.mnc output_labels.mnc --verbose --mask brain_mask.mnc

Segment using a specific atlas and low-resolution mode:

mrfseg.pl input_t1.mnc output_labels.mnc --atlas /path/to/atlas --lowres --clobber

AUTHOR

Vladimir S. Fonov. McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University.

COPYRIGHTS

Copyright (C) Vladimir S. Fonov and McGill University. Licensed under the terms of the GNU General Public License version 3 or later.

SEE ALSO

classify(1), em_classify(1), pipeline_classify.pl(1)